Metagenomic Analysis of the Deepwater Horizon Oil Spill
Introduction The Deepwater Horizon oil spill in the Gulf of Mexico resulted in the release of a hydrocarbon plume into the gulf water. This is beleived to have also caused a shift in the indigenous microbial composition of the gulf water. One microbe of particular interest, Oceanospirilales, was discovered early in the spill, however its functional role was unknown. Both deep sequencing of DNA and RNA, as well as single-cell genomics on the community level, were used to determine the specific impact of this deep sea genus in the microbial community closer to the surface. Methods Sample Collection Samples were collected from 3 sties, one of which was proximal (1.5 km from the wellhead), one of which was distal (11 km from the wellhead), and one that was uncontaminated (40 km from the wellhead). Methods The methods for this experiment are pictorially simplified by Figure 1. They include molecular analysis of the microbes as well as the metagenomics and metatranscriptomics procedures. These procedure included DNA and RNA extraction and amplification, emulsion PCR, sequencing, rRNA gene sequencing and analysis, research through a database (blastn), single cell sorting, entire genome amplification, and single cell Illumina sequencing. Also using infrared spectrometry the hydrocarbon concentration within the water was measured. Results Table 1- Diversity Metrics of Microbes in Samples a Species richness (Chao, 1984). b Confidence intervals (Chao et al., 1992). c Species richness (Chao et al., 2000). d Species diversity (Simpson, 1949). e Singeltons are species with only one individual. Doubletons are species with only two individuals (Colwell and Coddington, 1994). | | | | | | | |} Figure 2 and Table 1 are graphical representations of the abundance of different prokaryotic organisms with the proximal and distal samples. It shows that plume samples had a lower diversity of microbial life than the samples that were outside of the plume. It also shows a higher diversity at the proximal plume, becasue the microbes had longer to adapt to the oil in their environment. Figure 3 is an analysis of the metagenome pathway differences between the samples collected at the different sites. It shows that the entire pathway for the n-alkanes was represented and abundant in the samples that were taken from the plume. While less abundant aromatic molecule degredation enzymes were found within the plume samples, which is what the hydrocarbons would be form after being degraded. Figure 4 is a graphical representation of the gene abundance found in the samples for the genes need to degrade the hydrocarbons found in the plumes. From all this data a genome for the Oceanospirilales ''was drafted. From this drafted genome, that includes the genus's attraction to the plume, from the apperace of large absorptions around oil droplets obtained from the infrared spectrometry. Conclusion Dominant and active ''Oceanospirllales ''encode a complete pathway for the degredation of cyclohexane. The microbes metagenome was sequenced and a draft microbe was drafted that represents the motility, chemotaxis, and alkane degredation ability of the microbe. All of these allowed them to migrate to and establish colonies in the oil contaminated water of the Gulf of Mexico. References Mason, O., Hazen, T., Borglin, S., Chain, P., Dubinsky, E., Fortney, J., ... Jansson, J. (2012). Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ''The ISME Journal, 6'', 1715-1727. Retrieved November 12, 2014. ''The new science of metagenomics revealing the secrets of our microbial planet. (2007). Washington, D.C.: National Academies Press.